Jase Gehring

Denoising single-cell ATAC-seq data with Shannon entropy

This paper introduces a Shannon entropy-based method to filter high-quality nuclei in scATAC-seq data, improving signal-to-noise ratio and downstream analysis reliability.

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

The paper introduces SCOPE, an optics-free method to reconstruct 2D and 3D shapes using DNA barcode proximity graphs from sequencing data.

Quantifying orthogonal barcodes for sequence census assays

The paper introduces a modular approach and quality control metrics for improving barcode quantification in sequence census assays.

Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

The paper presents a whole-animal transcriptomic cell atlas of Clytia hemisphaerica using multiplexed scRNA-seq to study cell type plasticity under starvation.

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress is a simplified COVID-19 testing protocol that eliminates the need for transport media and nucleic acid extraction, achieving high sensitivity and specificity.

Modular and efficient pre-processing of single-cell RNA-seq

The paper presents a modular and efficient workflow for single-cell RNA-seq pre-processing using kallisto and bustools, demonstrating its flexibility for RNA velocity analyses.

Highly Multiplexed Single-Cell RNA-seq for Defining Cell Population and Transcriptional Spaces

The paper introduces a multiplexing method for single-cell RNA-seq that enables cost-effective analysis of large-scale perturbation experiments, revealing cell population and transcriptional changes not detectable by bulk methods.